Monday, December 4, 2017

Many of us like to believe that we are conceptually-oriented
researchers; our particular study organism(s) are just means to an end, the end
goal being to answer broad questions about how evolution or ecology works. But
our citation patterns suggest otherwise. We are more likely to read, and hence
more likely to cite, papers about organisms of direct relevance to our own
work. That results in some unfortunate conceptual balkanization. Case in point:
I’m writing an Annual Reviews paper on (non)parallel evolution, with several
co-authors. Collectively, we have all studied sticklebacks (though we have some
other study organisms in our history). So we tried very hard to diversify our
citations (taxonomically; I must admit I haven’t gone through and checked the gender
of first authors, for instance).

In one
section of the manuscript we discuss Langerhans and Dewitt’s 2004 AmericanNaturalist paper on Shared and Unique Features of EvolutionaryDiversification.In that paper’s
appendix they lay out a multivariate statistical approach to measure the extent
to which evolution has occurred in parallel across multiple replicates, or in a
unique direction in each replicate. That’s a very useful approach, that is very
conceptually general and widely applicable (hence its great fit to The American
Naturalist). So, I wanted to find a plant paper that cited this article, to use
as an example illustrating their analytical approach. The problem is, I found
only three plant papers out of the 200 that cited Langerhans and Dewitt (2004)
according to Web of Science (as of December 1 2017). That’s 1.5%.On the other hand, I noticed a suspicious
number of fish citations. So I went back and noted down the taxonomic focus of
each of the 200 papers citing their article (a few were reviews that had no
particular taxonomic focus, so I didn’t tally those). Here’s the breakdown
(sorted by # of citations):

Taxonomic group

Subgroup

# citations to L&D 2004

Fish

TOTAL:

118

Poeciliid

42

Stickleback

30

Centrarchid

6

Cichild

5

Salmonid

5

Other

30

Reptiles

TOTAL:

8

Lizards

6

Turtles

1

Snakes

1

Amphibians

TOTAL:

3

Salamanders

2

Frogs

1

Insects

6

Plants

3

Isopods

3

Mammals

2

Arachnids

1

Birds

1

Gastropods

6

The really striking thing here is how taxonomically biased
this is. The single genus Gasterosteus
has five times as many studies citing L&D than all studies of insects,
which collectively are of course at least as diverse as stickleback, and
possibly even as important from a practical standpoint.

Why is this
widely-applied method being effectively ignored by the vast majority of
researchers? I think the answer is pretty simple: because the original paper
was applying their method to study fish evolution, fish evolutionary biologists
were more likely to read it. Worryingly, this suggests that when we publish a
new method, we might reach the largest audience if we omit application of the
method to any one taxon (or, if we apply it to many diverse taxa). Equally
worringly, it suggests to me that because of our inherent taxonomic biases we
are missing the boat on many important ideas and methods.

The other
hypothesis of course is that parallel evolution may be an exceptionally hot
topic among fish biologists, especially stickleback- and Poeciliid-researchers.
Bandwagons happen. We tried really hard in our Annual Review manuscript to
branch out and cite studies involving something other than stickleback. That’s
hard both because this is the system we are collectively most familiar with,
and because this is such a great parallel-evolution system that many of the
leading studies on the topic use this organism.

There’s not
an easy solution to this, other than to check our biases at the door: when
writing, and when reading, ask yourself how diverse your citations (or paper
choices) are. Try to step out of your comfort zone, read something about an
organism you know nothing about, at least once a week if not more often. You’ll
learn a lot of biology in the process, and maybe get some new ideas that help
you step out of your taxonomic box.

Wednesday, November 29, 2017

In my capacity as (soon-to-be) Editor-In-Chief of The American Naturalist, I am also occasionally going to be posting on the AmNat Editor's Desk blog. Here, I'm just drawing attention to two new posts I put on that site.

1) As incoming EIC I wanted to articulate some aspects of AmNat's values and policies for our Associate Editors. They received a version of this by email. But I realized some of the points may be more broadly applicable, and useful to prospective authors as well. So, I also posted this as an open letter for anyone to read. You can read the full text here. Contents include some thoughts about:
- What the heck does AmNat publish (or not publish)?
- How fast should decisions be?
- When to decline without review?
- When to "decline without prejudice", and what exactly does that mean?
- When to send a revision back out to review, or not?
- The importance of value-added comments by Associate Editors' decision letters- Special Features in The American Naturalist- Progress in diversifying the AE board, thanks to Judie Bronstein and to be continued.2) This fall I had an extended conversation with Tim Parker from Whitman College, who is Co-organizer of the “Tools for Transparency in Ecology and Evolution” group. In this blog post I provide a summary of the TTEE standards and what AmNat will or will not do, to meet them.

While we are on the topic of this journal, here's an item of historical interest: a screen shot of the announcement in the 1960's when page charges were first instituted, to avoid having the journal go bankrupt and disappear.

Nearly every context for evaluation in academia (or, really,
anything) focuses on recent progress. What grants have your received in the last
five years? What papers have you published in the last five years? How many
students have you supervised in the past five years? I understand the logic behind
this approach and I am not necessarily criticizing it overall. After all, why
should a formerly influential faculty member get to keep hanging onto funding
and space for decades after they became “dead wood” in the department.

However, a few years ago, I encountered a pretty weird
version of this “what have you done lately” approach to evaluation. I was an
external member of a committee seeking to hire a professor. During the meetings
to evaluate candidates, one other member of the committee used, as a key criterion,
the trajectory of citations in Google Scholar to judge whether a person was “declining
in influence”. I found this criterion really weird as a person with few
citations in recent years could rank higher than a person with tons of citations
in the same year. (Of course, other valid reasons exist to not weight citations
highly in evaluations in general.)

And then I looked at my own Google Scholar profile. Lo and
behold, I was “declining in influence.” OK, fine, whatever: my happiness does
not depend on the trajectory of my citations.

Now, a few year’s later, however, it looks like this.

Now that I am on the upswing again, I am more convinced than
ever of the uselessness of the trajectory of citations for evaluation. Here are two
key reasons:

1. As citations always lag publications, the period of my
declining influence was – presumably – precisely the time I was publishing
papers that would prove to be increasingly influential.

2. Any career is likely to involve ups and downs in year-to-year
citation rates, which clearly do not reflect any real trend in “influence.”

In short, while I agree that old less-than-active folks
shouldn’t continue to take funds and space from more up-and-comers, citation
trajectories is NOT a way to make such assessments.

Saturday, November 25, 2017

Andrew Hendry: One of my great regrets as a scientist is
that I never got to know Dawn Phillip very well. She was of immense help to my
students and postdocs in Trinidad, far above and beyond just common courtesy.
Inspired by this regret, I asked my students – who knew her far better than I –
to provide their testimonials of appreciation. Before that, however, Anne
Magurran – Dawn’s PhD supervisor, friend, and frequently collaborator – provides
her own thoughts.

Anne Magurran: Dawn Phillip’s sudden death
last month means that we have lost a talented biologist, inspirational teacher,
role model and friend.

Dawn during her PhD field work. Photo by Anne Magurran

Dawn did her bachelor and masters’ degrees at
the University of the West Indies (UWI) in her native Trinidad and Tobago,
before joining me in Scotland for her doctoral research. She graduated
with a PhD from the University of St Andrews in 1998 with a thesis entitled
‘Biodiversity of Freshwater Fishes of Trinidad and Tobago, West Indies’. After
her PhD, Dawn secured a faculty position in Life Sciences at UWI. She had been
promoted just a short time before her death and was delighted to be rising
through the academic ranks.

Dawn was an extremely knowledgeable and
insightful ecologist. Like her PhD external examiner Rosemary Lowe-McConnell,
Dawn made important contributions to neotropical fish biology. Particularly
notable is her Zootaxa (1) paper - the authoritative overview of the
status and ecology of freshwater fish in Trinidad and Tobago and essential
reading for the many researchers drawn to the rivers of Trinidad’s Northern
Range. This paper, as well as the guide to freshwater fishes (2) that
resulted from her PhD research, and indeed all of her research output, was
under-pinned by meticulous field work, exceptional commitment to her
research and a deep appreciation of the ecology of organisms in their natural
environment. I think it is fair to say that I learnt as much from her as she
did from me.

Dawn always made me feel welcome in Trinidad
and I valued her friendship and the chance to catch up whenever I visited. We
continued to collaborate and had been working on a paper and exchanging emails
about it the day before her death. She was upbeat and looking forward to future
projects and challenges. It is hard to take in the fact that she is no longer
with us. I will miss her.

And now some testimonials, remembrances, and reflections
from my students and postdocs.

Jonathas Periera: “Sorry to upset your Saturday. I have to inform you
that Dawn died in her sleep sometime last night. We will update you as more
info becomes available. Sincerely yours, Mark Phillip.” This was how I
learned Dawn has passed away in October 28. Although I knew she had some sort
of health issues, this message in whatsapp was a shock. It still is. I had just
been with her in Trinidad, where I stayed five months doing field work. Dawn
saved my ass many times and greatly contributed to the (at least partial)
success of my field trip. Always smiling (even 4am in the morning!!), I feel
Dawn is perhaps the best representation of a true “Trini” to: always in good
vibes, no matter what. Dying over her sleep was perhaps the best way death
could find to take her life. My most sincere condolences to her family, friends, and the University of the West
Indies.

Felipe Perez-Jvostov: As everybody else starting a PhD, I spent the first several
months trying to understand my study system: who has done what, where have they
done it, what did they find. Confusion was commonplace – at least until my
first field season in Trinidad when start getting first hand experience. During
that trip I met Dawn Phillip. Dawn came to our research station to meet the
research crew. She had worked with guppies, Rivulus, and many other fishes that
have been so intensively studied in Trinidad, and she was always interested in
what people were up to, and how she could help. Her personality made it so easy
to get along with her – an air of familiarity that made you feel comfortable.
In my many subsequent trips, I would often chat with Dawn about my projects (or
more often the problems with them). She would always have a warm advice, and
calm me down with a smile. I was very sad to know of her passing. The research
community has lost a wonderful colleague, and those who knew her personally
have lost a dear friend that was always available to help – you just
needed to ask. At least for me, I will always remember that first time I met
Dawn, and how she would not say no to a « beastly cold Carib ».

Gregor Rolshausen: Dawn
was an indispensable and very helpful colleague of mine in Trinidad. She was an expert on
tropical fish communities, and introduced me to some of the most fascinating
ecosystems I have seen. A dedicated scientist and teacher at Western Indies
University, Dawn also had a passion for organizing field excursions and
connecting her students to international research projects. But above all, I
remember Dawn as a truly warm-hearted friend with a great laugh. It is very sad
to say goodbye this way.

Kiyoko Gotanda: Dawn was a
wonderful scientist and generous with her knowledge. Her research has been an
inspiration for my own work in Trinidad. She is a co-author of a guide to
freshwater fishes of Trinidad of which I had a black and white copy. Dawn
shared her colour plates with me, and the guide was invaluable in helping me
with identify the different species of fish I was sampling. My first field
season in Trinidad, I had wanted to explore some of the oily and non-oily sites
in the southern part of Trinidad. I had no experience working in that part of
Trinidad. Dawn provided maps, information, and one of her graduate students to
assist me in my sampling of these sites. Without her generosity and willingness
to collaborate, I would likely have never even found the sites! I am grateful
that I had the opportunity to work and interact with Dawn, and she will be
greatly missed.

Lea Blondel: I met
Dawn in 2016 during my third visit to Trinidad. We had already exchanged emails
before that, because I needed a local supervisor and because she helped a few
other students from my lab before. I immediately connected with her thanks to
her kind, generous and outgoing personality. Even if we didn’t interact much
when I was in Montreal, she always showed great interest to my project when we
met in Trinidad. The memory I will
keep with me is the day we spent together at her house this past March, talking
about exciting ideas and eating roti. The day was really warm so we got some
rest under the porch of her house, before driving along the east coast of
Trinidad where she shared some of her favorite places with me. It was a really
special day and I feel lucky to have had the opportunity to know the great
person and the great researcher she was.

Dawn during field work just last year. Photo by Lea Blondel.

-----------------------------------

I hope others who have benefited from Dawn’s kindness
and help will add comments to this post.

Monday, November 13, 2017

(NOTE: The following post was
written by Tania Tasneem, a middle school science teacher in Texas. Tania
worked in Dan Bolnick's lab for three summers. In 2006 she was supported as an
REU student (Research Experience for Undergraduates), paid by a REU supplement
to an NSF grant. Shortly after, she graduated and began teaching middle school.
In 2013 she returned as an RET (Research Experience for Teachers) to do both
field work in British Columbia, and lab work in Austin. Her salary
came from the fantastic 'Research Experience for Teachers' (RET) program that
NSF funds as supplements to new or existing grants, in this case a
collaborative grant between Dan Bolnick, Andrew Hendry, and Katie Peichel.
Tania returned in 2014 for an additional summer's RET, this time exclusively
doing lab work in Austin identifying fish stomach contents and parasites from
the samples she helped collect in 2013. As a result of this work, Tania is a
co-author on a Nature Ecology & Evolution paper, and on another manuscript
in preparation. Since 2013, the Bolnick lab has hired 7 RETs to
participate in research, usually in pairs, or paired with an undergraduate
studying to become a K-12 STEM teacher. Most of these teachers have ended up as
co-authors on one or more published articles. The following essay conveys the
RET's perspective on this experience. I have posted this without editing,
to clearly convey both the pros and cons of the RET experience in the hopes
that this information can improve other researcher-teacher interactions.- Dan
Bolnick, Nov 8, 2017)

The author, Tania Tasneem, as an REU student in summer 2006 in British Columbia

I recently went to a training
for seasoned teachers on how to best support new teachers during their first
year. Figure 1 shows the progression of a first year teacher’s attitude toward
teaching and was projected at the end of the day long training to remind us of
all of the emotions a first year teacher encounters. As the first
semester of my 11th year comes to an end, I can assure you that
this data holds true to most teachers every single school year. The figure also
mirrors some of the emotions I encountered during my first field/lab experience
in the Bolnick lab as an REU during the summer of 2006 and again as an RET
summer of 2013 and 2014.

For each of these emotions, I
have tried to reflect on my mindset/paradigm shifts as an REU (in my early 20s
and a novice teacher) and as an RET (in my early 30s with 8-9 years of teaching
experience) about joining the project, doing field work, my lab experience
during the summer, and the impact on my teaching practices. I’ve tried to give
a brief explanation of what that phase is like as a teacher and how it is
related to the field/lab experience in the summer from the perspective of a
novice teacher (REU experience) and a veteran teacher (RET experience).

Anticipation Phase
(Before going into the field)

The anticipation stage begins
during the student teaching portion of pre-service preparation. My first field
experience was the summer before I started my student teaching semester so I
can definitely relate to feelings of excitement and anxiousness as I became
closer to the start of a school year with a mentor and being in the classroom
every day. New teachers, myself included entered with a tremendous commitment
to making a difference and a somewhat idealistic view of how to accomplish
these goals. Seasoned teachers on the other hand are more anxious about new
district and campus initiatives, administrative/teacher turnover and impacts
for their campus, what their new student needs will be for the upcoming school
year. This feeling of excitement carried me through the first week of field
work and carries me through the first weeks of school every year.

Survival Phase (In the
field)

During
the survival phase, teachers (new and seasoned) are overwhelmed, bombarded with
a variety of problems and situations they had not anticipated, and trying to
keep their heads above water. New teachers are learning a lot at a very rapid
pace and consumed with the day-to-day realities and routines of teaching. There
is little time to stop and reflect on their experiences. It is not uncommon for
new teachers to spend up to seventy hours a week on schoolwork. While seasoned
teachers can manage these realities a little bit better, most seasoned teachers
have a similar work load or work as mentors to help new teachers survive this
phase. There is little time to stop and reflect on their experiences. It is not
uncommon for new teachers to spend up to seventy hours a week on schoolwork.

Particularly
overwhelming is the constant need to develop curriculum. Veteran teachers
routinely reuse excellent lessons and units from the past. New teachers, still
uncertain of what will really work, must develop their lessons for the first
time. Even depending on unfamiliar prepared curriculum such as textbooks, is
enormously time consuming.

Disillusionment
Phase (Field season almost over)

This is
the “I’ve made a terrible mistake, what was I thinking?!?!?!” phase. After six
to eight weeks of nonstop work and stress, new teachers enter the
disillusionment phase. The intensity and length of the phase varies among new
teachers. The extensive time commitment, the realization that things are
probably not going as smoothly as they want, and low morale contribute to this
period of disenchantment. New teachers and veteran teachers alike question both
their commitment, competence, and career choices during this phase.

Rejuvenation Phase (field
work is over, to the lab)

The rejuvenation phase is
characterized by a slow rise in the new teacher’s attitude toward teaching.
Having a break makes a tremendous difference for new and veteran teachers
alike. It allows them to resume a more normal lifestyle, with plenty of rest,
food, exercise, and time for family and friends. This vacation is an
opportunity for teachers to organize materials and plan curriculum. It is a
time for them to sort through materials that have accumulated and prepare new
ones. This breath of fresh air gives teachers a broader perspective with
renewed hope.

During this phase we are ready to put past problems behind
us, have a better understanding of the system, an acceptance of the realities
of teaching, and a sense of accomplishment. Through their
experiences in the first half of the year, teachers gain new coping strategies
and skills to prevent, reduce, or manage many problems they are likely to
encounter during the second half of the year. Many feel a great sense of relief
that they have made it through the first half of the year. During this phase,
teachers have the time to focus on curriculum development, long-term planning,
and teaching strategies.

Reflection Phase (End of the summer lab/field season and
on to the new school year)

The reflection phase is a particularly invigorating time for
teachers. Reflecting back over the year, allows us to highlight events that
were successful and those that were not. We think about the various changes
that we plan to make the following year in management, curriculum, and teaching
strategies. The end is almost in sight, and we have almost made it; but more
importantly, a vision emerges as to what our next year will look like, which
brings a new phase of anticipation.